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This is a far reaching change that I would be rather conservative about. I'm happy to probe the community but maybe the ability to change the global configuration to include infinity is enough?
@op…
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## Target functionality
There is a problem known as gap-filling which is used to consider what new reactions on could add to a model to improve an objective.
This is similar to knock-out which con…
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Otherwise there will be cyclic referencing. Adding `__del__` methods to handle solver-specific cleanup routines will prevent the garbage collector from collecting these cycles.
Should solve #125 an…
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BiGG provide a very handy universal model at : http://bigg.ucsd.edu/data_access
The JSON format is supposed to be a COBRA-compliant model, however it does not respect the schema from : https://github…
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SBML documentation is outdated on https://cobrapy.readthedocs.io/en/stable/io.html. E.g.,
* remove mentioning of lxml
* document python-libsbml correctly
* SID not documented correctly (patterns…
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In cobrapy we obviously use python-libsbml quite a bit and when running our test suite with pytest we get thousands of deprecation warnings coming from libsbml. For anyone else coming across this issu…
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Presently, `ChangeAttribute.newValue` has data type of `string`. It would be helpful to keep track of the true data type (e.g., Boolean, integer, float, string, etc.). This would facilitate semantic i…
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hello,
Code used: memote report snapshot --filename "report_model.html" ~/Desktop//model.xml
Error:
Traceback (most recent call last):
File "/home/carol/miniconda3/envs/metabolic_model_env…
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Hi,
I'm trying to gauge the general interest in and start a discussion around extracting some of cobrapy's core functionality into a separate package. The goal of the new package would be a faithfu…
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_From @zakandrewking on June 28, 2017 22:4_
Hi All:
I hope this is not a rehash of a previous conversation, but I could not find it, so here we go :)
Can we support non-integer charges in SBML …